CITE-seq

High piRNA abundance is a hallmark of evolutionarily persistent piRNA-producing loci.

The paper identifies high piRNA abundance as a key feature of evolutionarily persistent piRNA-producing loci across mouse and primate species.

A Reproducible Pre-Transplant γδ T-cell Effector Signature Reveals Immune-Metabolic Programs Associated with Kidney Allograft Rejection

The paper identifies a pre-transplant γδ T-cell effector signature associated with kidney allograft rejection using multi-omics data from transplant recipients.

TSNR: Protein-Specific Signals with Broad Molecular Context for Spatial Protein Prediction

The paper introduces TSNR, a method for spatial protein prediction that uses protein-specific signals and broad molecular context, achieving high correlation on a benchmark.

Knockdown of the long non-coding RNA DNAAF3-AS1 activates the p53 pathway and remodels the H3K36me3 landscape

This study shows that knocking down DNAAF3-AS1 reduces gene-body H3K36me3, activates the p53 pathway, and alters promoter usage in apoptosis-related genes.

High-resolution analysis of T cell subsets, clonality, and trajectories in psoriasis

This study analyzes T cell subsets, clonality, and trajectories in psoriasis using single-cell RNA and TCR sequencing, revealing tissue-specific and shared features of the T-cell repertoire.

Building virtual cell dynamics that evolve with biological measurements

CellCompass, an agentic AI system, models cell dynamics from single-cell measurements and improves predictions by integrating new biological constraints and experimental data.

NK Cells Engineered with a Chimeric Antigen Receptor Delay HIV Rebound and Reshape HIV Reservoir Composition

This study shows that engineered NK cells with a CD4-based CAR delay HIV rebound and alter the reservoir's composition in humanized mice.

Single-Cell Sequencing in Pediatric Acute Leukemia: A Systematic Review of Biologic Insights and Translational Potential

This review evaluates single-cell sequencing findings in pediatric acute leukemia, highlighting insights into clonal evolution, chemoresistance, and immune dynamics, while noting limitations in study design and bias.

Recurrent leukaemia stem cell states define the antigenic landscape of paediatric Acute Myeloid Leukaemia

This study identifies three leukaemia stem cell subtypes in paediatric AML and shows that combining CLEC12A and CD84 targets all subtypes while sparing healthy cells.

A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

Insulin-binding B cells can arise in early-stage type 1 diabetes individuals in the absence of somatic hypermutation or insulin autoantibody seropositivity

The paper identifies anti-insulin B cells in early-stage T1D patients without autoantibodies or somatic hypermutation, showing their role in autoimmunity.

A computable probability landscape for T cell receptor repertoire sampling and comparison

The paper introduces BEAM, a probability model for TCRβ sequences that enables depth-aware sampling calculations and interpretable repertoire comparison.

Stealth CAR-Tregs evade CD3 antibody therapy and skew immune responses toward regulation

This study shows that TRAC-/-CAR-Tregs survive CD3 antibody therapy better than TRAC+/+CAR-Tregs, shifting immune responses toward regulation.

Evidence for reduced somatic T-cell receptor sequence diversity profiles among Midwestern Amish in an aging cohort study

The paper examines T-cell receptor sequence diversity and HLA alleles in Midwestern Amish participants to explore associations with Alzheimer's disease and cognitive status.

Heterogeneity of HCMV-Specific CD8+ T Cells is Established Early in Infection, Clonally Encoded, and Stable Over Time

The paper tracks CMV-specific CD8+ T cells over time to show that clonal diversity and phenotypes are established early and remain stable during chronic infection.

Antigen-aware TCR embeddings reveal conserved immune patterns for personalized immune monitoring

TCRmeta integrates antigen specificity with TCR repertoires to enable cross-individual and longitudinal immune monitoring by revealing conserved patterns and technical variation robustness.

Discovery of frameshift-associated TCRs following personalized neoantigen vaccination in a patient with osteosarcoma

The paper reports the discovery of TCRs specific to vaccine peptides in a patient with osteosarcoma following personalized neoantigen vaccination and in vitro expansion.

Limits of marker information transfer]{Limits of marker information transfer in cross-panel cytometry imputation

This study evaluates the limits of marker information transfer in cross-panel cytometry imputation, finding that imputation preserves broad lineage classification but not fine-phenotype details, and that patient matching improves cross-platform distribution recovery.

Single-Cell Proteo-Transcriptomic Profiling Uncovers Post-Translational Regulatory Layers in Human Hematopoiesis

This paper uses single-cell proteo-transcriptomic profiling to reveal post-translational regulatory mechanisms in human hematopoiesis, showing that protein-RNA correlations and transcription factor dynamics provide insights into lineage commitment and fate decisions.

Repeated malaria exposure reprograms Vδ2+ γδT cell chromatin accessibility and immune function toward a reversible hyporesponsive state

Clonally expanded CD8 T cells in AML adopt an NK-like program distinct from canonical exhaustion

Optogenetic BMP4 models symmetry breaking and primitive streak formation in hPSCs

This paper introduces LightBMP, an optogenetic tool to control BMP4 in hPSCs, showing spatial BMP4 patterns can drive symmetry breaking and primitive streak formation without mechanical cues.

Rank-Preserving Alignment Enables Cross-platform Learning and Phenotyping for Single-Cell and Spatial Proteomics

RAMP improves cross-platform proteomics analysis by preserving protein expression order, enhancing cell-type annotation and prediction across multiple cancer types.

Tfh dysfunction is associated with poor responses to HBV vaccination

HBV vaccine-draining lymph node biopsies tie low antibody titers to reduced, interferon-skewed GNG4+ germinal center T follicular helper cells; public B cell clonotypes did not track response.

ClonoDynamics enables replicate-resolved inference of longitudinal T cell receptor repertoire dynamics

ClonoDynamics distinguishes estimator-induced patterns from true longitudinal variation in T cell receptor repertoires using replicate-resolved analysis.

Peripheral Immune Alterations and T Cell Clonal Dynamics Across the Parkinson's Disease Spectrum

This study uses single-cell RNA sequencing and TCR profiling to analyze immune changes in Parkinson's disease across different stages and identifies sex-dependent immune alterations and TCR diversity.

Cross-species molecular stratification enables T cell receptor diagnosis of Parkinson's disease

This paper stratifies Parkinson's disease patients using T-cell receptor repertoires and develops classifiers that achieve high AUC for subtype diagnosis.

ScProteoAgent enables natural-language-driven single-cell proteomics analysis and interpretation

ScProteoAgent translates natural-language requests into single-cell proteomics analyses, preserving analytical state and enabling follow-up queries with high benchmark performance.

CryoMV: Structure-Prior-Guided Modeling and Real-Particle Validation of Continuous Conformational Transitions in Cryo-EM

CryoMV generates and validates continuous protein conformations from cryo-EM data using structure priors and real-particle validation, achieving high resolution and robustness on benchmark datasets.

Genetically inducible coordinators of cytokine signaling pathways for interrogating T cell motility

The paper develops CAMPs, genetically inducible receptors to control cytokine signaling in T cells, to study motility and signaling pathways without paracrine interference.